Hooker Steve Thompson wrecked the Reivers' hopes of pulling off a shock Heineken Cup triumph in a Franklins Gardens thriller.
The Scots had battled bravely to keep alive their chances - only for the England World Cup hero to snuff out their challenge with his quickfire try-double.
Now the Borders must notch an unlikely home-and-away success against French champions Biarritz to get a ticket to the knock out stages.
Borders were under the cosh from the outset, however Saints could not turn heavy pressure into instant points.
A combination of poor passing and lack of communication in the backline allowed the visitors to keep their line intact during the nervy opening exchanges.
Reivers stand-off Stephen Jones thought he was on course for a dramatic interception try as he raced clear from his own danger-zone.
But French referee Christophe Berdos ruled offside against centres Ben MacDougall and Nick De Luca.
And former All Black Carlos Spencer slotted the simple penalty to edge the home troops in front.
Even better was to come for Saints just two minutes later when another ex-New Zealand Test hero, Mark Robertson, capitalised on slack narrow-side Reivers defence to scuttle through for the first try.
The scrum-half had ample time to carry the ball behind the posts, handing Spencer another formality of a kick.
Fit-again England winger Ben Cohen then stretched the Borders markers with two bullocking runs as Northampton stepped up the territorial domination.
The Scots at last earned a breather with a penalty for illegal handling on the ground at a ruck.
And Calum MacRae stepped up confidently to slot the 45-metre effort to break his side's duck.
There was more encouragement for the underdogs when new signing Brendon Daniel surged deep into enemy territory - only to lose his footing and momentum at a crucial moment.
Borders hooker Ross Ford was lucky to dodge a yellow card after appearing to land a punch on Paul Tupai.
And the Reivers were back on the rack as Spencer slotted his second penalty from close range.
Their plight deepened when Samoan lock Opeta Palepoi was carried off on a stretcher with what looked like a back or neck problem and replaced by Scott Newlands.
Even worse was to come as MacDougall was sent to the sin-bin for a high challenge.
Saints upped the pace in the build up to the interval and Rhodri Davies was inches away from claiming a second touchdown as he chased a Spencer chip
There was still time for MacRae to keep the Reivers alive with another penalty awarded by backchat by Darran Fox.
The second half was even more incident packed.
Tupai seized back the initiative for the Saints with an opportunist try from close quarters. But Reivers replied with a remarkable score by winger Simon Danielli - desperate to get back into the Scotland set-up.
Danielli received the ball 10 metres inside his own half, left the home defence for dead with a series of dazzling sidesteps and diversions - and gleefully plonked the ball down for MacRae to convert burst the contest wide open again.
However, it was all Saints from that moment on, with referee Berdos taking a major hand. He handed Northampton a penalty try for alleged interference with the boot.
Then prop Gavin Kerr was yellow carded for a mystery offence.
And the stage was left to Thompson, who killed off the Reivers challenge with his double whammy.
There was more agony for the Reivers when substitute Scott Newlands was denied a try by the TV official.